Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

S Ou, W Su, Y Liao, K Chougule, JRA Agda… - Genome biology, 2019 - Springer
Background Sequencing technology and assembly algorithms have matured to the point
that high-quality de novo assembly is possible for large, repetitive genomes. Current …

A chromosome conformation capture ordered sequence of the barley genome

M Mascher, H Gundlach, A Himmelbach, S Beier… - Nature, 2017 - nature.com
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions
since the dawn of agriculture. Their large genomes are characterized by a high content of …

Transcriptome variation in human tissues revealed by long-read sequencing

DA Glinos, G Garborcauskas, P Hoffman, N Ehsan… - Nature, 2022 - nature.com
Regulation of transcript structure generates transcript diversity and plays an important role in
human disease,,,,,–. The advent of long-read sequencing technologies offers the opportunity …

LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons

S Ou, N Jiang - Plant physiology, 2018 - academic.oup.com
Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The
identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the …

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

FW Li, P Brouwer, L Carretero-Paulet, S Cheng… - Nature plants, 2018 - nature.com
Ferns are the closest sister group to all seed plants, yet little is known about their genomes
other than that they are generally colossal. Here, we report on the genomes of Azolla …

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

H Badouin, J Gouzy, CJ Grassa, F Murat, SE Staton… - Nature, 2017 - nature.com
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for
climate change adaptation, because it can maintain stable yields across a wide variety of …

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

D Libkind, N Čadež, DA Opulente… - FEMS Yeast …, 2020 - academic.oup.com
In recent years,'multi-omic'sciences have affected all aspects of fundamental and applied
biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate …

Comparative genomics of the major parasitic worms

Nature genetics, 2019 - nature.com
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating
chronic infections of humans and animals, decimate crop production and are a major …

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

M Griesmann, Y Chang, X Liu, Y Song, G Haberer… - Science, 2018 - science.org
INTRODUCTION Access to nutrients such as nitrogen is required for plant growth. Legumes
and nine additional plant families benefit from the nitrogen-fixing root nodule (NFN) …

Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits

N Liu, X Lyu, X Zhang, G Zhang, Z Zhang, X Guan… - Nature Genetics, 2024 - nature.com
Peas are essential for human nutrition and played a crucial role in the discovery of
Mendelian laws of inheritance. In this study, we assembled the genome of the elite …